1) What is the best format to export out of FCP for Illustrator?
- pict, psd, tiffs or jpeg best quality sequence should all work. i use jpegs. you probably don't neeed 30 fps. i frequently use as few as 4-6 fps and apply afx frame blending when you play back the processed sequence.

2) What is the best way to apply the SAME effect to all files in the image sequence?
- do a first trace manually, export/save the trace pallette/swatches and settings you want to use from illustrator.

3) Am I basically asking how to BATCH PROCESS?
- use adobe BRIDGE. upen the folder in bridge that you exported the FCP sequence of stills from, select all the stills, go to TOOLS>illustrator>live trace, choose the trace preset you made and the destination size/location etc. export in any of the formats you imported. you should end up with another sequence of processed stills that you can re-import to FCP and edit or adjust playback speed there.